I'll try to get to all your questions and points as best as possible, to help to understand it better.

I don't want it to be one or the other. I'll try to give a few examples for this. Think of it like a Mega Man game where he was transported to a fantasy setting, except this setting is Final Fantasy 1. With that in mind, think of Gargoyle's Quest. The role-playing aspects came through when exploring the towns and the world map, talking to NPCs for quests, buying items, and getting into random encounters on the map.

Now, onto the actual combat side of things. When you entered combat in GQ, just like in FF, the perspective and gameplay changed. Like GQ, exploring the world map and towns would be played with the same perspective in this Mega Man game, and like GQ you would be able to talk to characters for information and quests, buy certain things, etc. The random encounter aspect of GQ would be used as well - only on the world map and played out in a side-scrolling mini-level. When you are in dungeons, the gameplay would be a side-scrolling action-platform like GQ's areas. The only difference is the layout would have to take in the original Final Fantasy game's dungeons: if it was a four story dungeon in FF, it would be like a four story Mega Man level; it would also have the same chests and items, though the items would be balanced if they have to.

Next, spells and abilities. In GQ, Firebrand had different projectile attacks, starting with his basic Fire attack, which would be Mega Man's Mega Buster. Firebrand would go on to get the Blockbuster, Claw, and Darkfire projectile attacks, each having a certain thing to set them apart, other than the higher damage, like the Blockbuster being able to break blocks and the Claw forming a solid substance to reach new areas.

In terms of the basic element-based spells in Final Fantasy like Fire, Blizzard, and Thunder, they would be bought or learned like the typical RPG. Since this game is using FF monsters, it would also be using their weaknesses too, so its not just the Bosses that have a certain weakness. However, like any RPG, you need to know how to balance the use of these abilities because of energy, or MP.

Defeating a boss would give you a new abilities. The specific boss weakness would be element based, so its not just that you are using an attack learned from another boss on them, it's that it would be the strongest attack of that element. Also, some of these spell attacks could have certain features that would be used for exploration, like in GQ, on top of its offensive aspect, and this is where the Metroidvania and dungeon progression comes into play. Need to get over a large expanse of water? Freeze it by shooting the water with Blizzard.

Now on to Summons and Limit Breaks. Final Fantasy 1 doesn't have any.

And now, to that last piece of advice. While I know for the most part everything I want in the game, it doesn't mean I'm going to throw everything into it. Like in any development of a game, things always change from conception through production, and it would work the same way here.

Alright, I have a better understanding of what you're trying to accomplish and I have one more piece of advice/wisdom I wish to share.

When making this game, remember to adjust the game's length to accommodate the added length of each encounter. Remember that a Final Fantasy game generally takes 50 hours and places players through hundreds of encounters with each encounter taking 1 minute on average to complete. I don't think many people would be interested in playing a similarly lengthy game but with each encounter replaced by a 5 minute long stage on average to complete. Maybe take a page from the Zelda 2 handbook and have encounters in the wild be a generic screen that can be entered and exited in less than 30 seconds if you're not screwing around, and include safety zones like roads to allow players areas where random encounters wont trigger any fights (you might want to add some roads or designate some kind of area that's safe to travel on without fear of random encounters early on at least, since most of FF1's overworld map is maze like wilderness). Besides, this will save you on battle arenas to design and program.

Beyond that though, my only suggestion is to take this idea of yours a step further and make it a Captain N: The Game Master game. Why stop at Final Fantasy, Mega Man, and Gargoyle's Quest when you can toss in some characters and references to Kid Icarus, Punch Out, Metroid, Castlevania, and maybe the occasional appearance by Link and Gannon? It'll be every 80's kid gamers' dream come true if you pull it off.

Alright, I have a better understanding of what you're trying to accomplish and I have one more piece of advice/wisdom I wish to share.

When making this game, remember to adjust the game's length to accommodate the added length of each encounter. Remember that a Final Fantasy game generally takes 50 hours and places players through hundreds of encounters with each encounter taking 1 minute on average to complete. I don't think many people would be interested in playing a similarly lengthy game but with each encounter replaced by a 5 minute long stage on average to complete. Maybe take a page from the Zelda 2 handbook and have encounters in the wild be a generic screen that can be entered and exited in less than 30 seconds if you're not screwing around, and include safety zones like roads to allow players areas where random encounters wont trigger any fights (you might want to add some roads or designate some kind of area that's safe to travel on without fear of random encounters early on at least, since most of FF1's overworld map is maze like wilderness). Besides, this will save you on battle arenas to design and program.

Beyond that though, my only suggestion is to take this idea of yours a step further and make it a Captain N: The Game Master game. Why stop at Final Fantasy, Mega Man, and Gargoyle's Quest when you can toss in some characters and references to Kid Icarus, Punch Out, Metroid, Castlevania, and maybe the occasional appearance by Link and Gannon? It'll be every 80's kid gamers' dream come true if you pull it off.

On the topic of the length of random battles: the random battles in Gargoyle's quest were small and short as well, about the right scale for what would be in this game. However, the variety in those levels were limited due to the size they could work with, something I hope to do better with. I wouldn't make the stages bigger, necessarily, just more varied and interactive.

About the Captain N idea, I want to focus on incorporating just these two games right now. However, I have thought about having the game be apart of a bigger storyline and universe, so the potential is there for more games down the line, not just Mega Man and FF. I definitely would love to use Castlevania with another game in the future, that's for sure.

And if it turns out I'm not able to pull this off, I might still try going at it from a different angle, like a web-comic - if you want an idea of how that could work, look here heroes-comic.com

Instead of only using the original Mega Man game in the first game in the Mega Man X Final Fantasy series, I think it would make more sense to use another Mega Man NES game for the foundation, since they might have better features and graphics.

Anyone know of all the NES Mega Man games, 1-6, which one would be the easiest to hack? Perhaps one game having a better editor than another? I'd like to start with the easiest one in that regard, in my first attempt at creating this game.

Instead of only using the original Mega Man game in the first game in the Mega Man X Final Fantasy series, I think it would make more sense to use another Mega Man NES game for the foundation, since they might have better features and graphics.

Anyone know of all the NES Mega Man games, 1-6, which one would be the easiest to hack? Perhaps one game having a better editor than another? I'd like to start with the easiest one in that regard, in my first attempt at creating this game.

Honestly. At this point in time, I wouldn't be surprised if there was some kind of Mega/Rock Man Maker software given how many MM based fan projects there are out there.

That said, outside of 6's Rush Armors, 4 was the last NES Mega Man game to see any sort of noticeable mechanical changes with the addition of the Charge Shot, headbanging, and the inventory UI used in every NES MM game since. Really though, the NES games are almost virtually identical to each other to begin with, especially when you consider rate that Capcom cranked them out (not to mention how they repurposed the engine for their Disney licensed games, and eventually rebuilt it for MMs 9 & 10).

And yeah, all the NES Megamen are tweaks on a formula. A formula that works well, mind you.

Also, I'm pretty sure MM3 was forced out the door incomplete. The glitched scanline in the fight with Wily Machine 1, the extended intro music with no intro cutscene to go with it, and the stationary Rush Jet that's animated like it's in constant motion(which is how the Jet Sled in MM2 and the Rush Jet in every other Megaman game ever behave) make me think there was another layer of polish that was supposed to be there.

And yeah, all the NES Megamen are tweaks on a formula. A formula that works well, mind you.

Also, I'm pretty sure MM3 was forced out the door incomplete. The glitched scanline in the fight with Wily Machine 1, the extended intro music with no intro cutscene to go with it, and the stationary Rush Jet that's animated like it's in constant motion(which is how the Jet Sled in MM2 and the Rush Jet in every other Megaman game ever behave) make me think there was another layer of polish that was supposed to be there.

Well as much head banging as 8-bit sprites are capable of (or more specifically, the Wire item requires you to press up so that Mega Man can look upwards to use, then you just tap Up repeatedly to get him to rock his head up and down).

But yes, MM3 was the one that was rushed out the door unfinished which is why Inafune went on record to say that it was his least favorite. It was also the last NES game to even attempt to change the formula with the revisited stages and resurrected bosses from 2 and the last classic MM game to not feature the Wily saucer as the final boss (save for MMV(GB) every other classic MM game since has ended on that exact same fight). And this was after MM2 which was made as a side project and not as something Capcom green lighted til it was finished.

The 25 and a half yearlong tl;dr is that there really hasn't been a point in the MM franchise's history where Capcom either wanted to shelve or exploit it.

And yeah, all the NES Megamen are tweaks on a formula. A formula that works well, mind you.

Also, I'm pretty sure MM3 was forced out the door incomplete. The glitched scanline in the fight with Wily Machine 1, the extended intro music with no intro cutscene to go with it, and the stationary Rush Jet that's animated like it's in constant motion(which is how the Jet Sled in MM2 and the Rush Jet in every other Megaman game ever behave) make me think there was another layer of polish that was supposed to be there.

Well as much head banging as 8-bit sprites are capable of (or more specifically, the Wire item requires you to press up so that Mega Man can look upwards to use, then you just tap Up repeatedly to get him to rock his head up and down).

But yes, MM3 was the one that was rushed out the door unfinished which is why Inafune went on record to say that it was his least favorite. It was also the last NES game to even attempt to change the formula with the revisited stages and resurrected bosses from 2 and the last classic MM game to not feature the Wily saucer as the final boss (save for MMV(GB) every other classic MM game since has ended on that exact same fight). And this was after MM2 which was made as a side project and not as something Capcom green lighted til it was finished.

The 25 and a half yearlong tl;dr is that there really hasn't been a point in the MM franchise's history where Capcom either wanted to shelve or exploit it.

On the last part, I have theory about the lack of games and the many cancellations. Capcom, in my opinion, seems to be suffering an identity crisis, concerning the Japanese vs. Western game design. It might be that they are taking there time, to figure out the best way to proceed with the franchise. Also, did anyone read about the cancelled Mega Man FPS game which was developed by Armature Games? Michael McWhertor wrote a great article about it here http://www.polygon.com/2013/4/9/4179628/mega-man-fps-maverick-hunter

Before I go, I need to ask one thing. While I still want to work on the Mega Man x Final Fantasy game, I wanted to look into some simple hacking projects, be it simple music hacks or sprite hacks, or changing text. Little projects for learning purposes. But I also want to try hacking a SNES rpg, and wanted to know which games have the best hacking utilities and editors.

This episode has to do with the NPC character in the Legend of Zelda on the NES saying "The 10th enemy has the Bomb" and how its about killing ten enemies in a row without getting hit, and the tenth will give you a bomb.

Both of these were figured out by people wanting to learn the ins and outs of their favorite games, and so if you do really want to look into hacking your favorite game, I thought this might give you some inspiration, as you can get interesting results in your studies.

This episode has to do with the NPC character in the Legend of Zelda on the NES saying "The 10th enemy has the Bomb" and how its about killing ten enemies in a row without getting hit, and the tenth will give you a bomb.

Both of these were figured out by people wanting to learn the ins and outs of their favorite games, and so if you do really want to look into hacking your favorite game, I thought this might give you some inspiration, as you can get interesting results in your studies.

You don't need to worry about getting hit or not. Just by going from the design docs that have cropped up over the years, there are specifically three or four enemy drop tables used throughout the game. Whenever you score a kill the game looks at the ones place on a hidden kill counter and compares it to the drop table appropriate to the enemy you just offed. Each table contains 10 items, 0-9 respectfully, before looping around again and of those tables one has bombs on it. You just have to find the enemy with the right drop table assigned to it and make it your tenth kill (or kill ten of them) and hope the RNG rolls in your favor.

In other words, none of the fun units. No J9 and the Space Car, no Gravion and its Maid-rush, and not even some G Gundam for some Master Asia punching out Mecha Beasts action.

Man, you want fun, take an Eva into any map in Super Robot Wars F.

The AT field in F actually soaks more damage than their starting hit points in 2/3s of the Evas, so they are completely immune to any attack that isn't powerful enough to 1-shot them.

Then you put a minovsky craft on Asuka's unit, throw her into a swarm and laugh as the crimson reaper(three times deadlier than a standard reaper) delivers invincible counterattack axe-murderess death from above.